Jim Mullikin, Ph.D.
Cancer Genetics and Comparative Genomics Branch
Comparative Genomics Analysis Unit
NIH Intramural Sequencing Center
B.S. Purdue University, 1982
M.S. Purdue University, 1984
Ph.D. Delft University of Technology, Holland, 1993
Dr. Mullikin's educational background is in electrical engineering, having earned a B.S. and an M.S. from Purdue University, and in physics, with an emphasis in image processing and pattern recognition, having earned a Ph.D. from Delft University of Technology, Netherlands. Dr. Mullikin first began to apply these skills to the genomics field in 1997, just as the Human Genome Project was scaling up. He has been involved in many aspects of the Human Genome Project as well as numerous other genome projects. His Sequence Search and Alignment by Hashing Algorithm (SSAHA) greatly sped up the process of SNP discovery, first for The SNP Consortium Project and later in the International HapMap Project. Dr. Mullikin also developed a whole-genome assembly program, called Phusion. Dr. Mullikin develops and utilizes computer programs to analyze large data sets generated by systematic DNA sequencing projects. A highly skilled computational geneticist, he collaborates extensively with biomedical researchers, developing data analysis methods specifically tailored for each class of project.
Applied math and physics, signal and image processing, computer science and statistics: these are a few areas of Dr. Mullikin's educational background that have enabled him to tackle a diverse range of projects, from measuring cardiac output from saline dilution curves (Voorhees et al., Med Instrum 1985) to measuring the surface area of objects detected in 3-D images (Mullikin and Verbeek, Bioimaging 1993), and from automated tracking of sample lanes on ABI377 gel images to assembly of whole mammalian genomes from Sanger sequence data. His primary interests are in developing novel and efficient algorithms using high-performance compute clusters to reduce large data sets into meaningful results.
He first started working in the field of genomics at the Sanger Center in 1997. Over five years there, Dr. Mullikin's research group improved the restriction digest fragment analysis package called "Image", custom-modified 60 ABI377 sequencing machines to scan 96 lanes, developed a blazingly fast sequence aligner called SSAHA and its genomic sequence variation detection version called SSAHA-SNP (Ning et al., Genome Res 2001), and developed a whole-genome assembly algorithm called PHUSION (Mullikin and Ning, Genome Res 2003). Dr. Mullikin was also the head of the production software group, which developed the laboratory information management system for tracking DNA sequence samples, barcode driven sample loading, automated data transfer off the sequencing machines to the central computer cluster, and automated assembly of the sequence data for the BAC clone-based sequencing of the C. elegans, human, mouse and zebrafish genomes. Since joining NHGRI in 2003, he continued his involvement in large-scale collaborative projects (The International HapMap Consortium, Nature 2005 and 2007; ENCODE Project Consortium, Nature 2005).
At NHGRI, Dr. Mullikin's research group developed a medical sequencing analysis pipeline, which at its peak in 2008 processed over three million Sanger-based sequence reads across tens of projects (Lagresle-Peyrou et al., Nat Genet 2009; Biesecker et al., Genome Res 2009; Kang et al. N Engl J Med 2010; McLaughlin et al., Am J Hum Genet 2010; Davis et al., Nat Genet 2011; Bell et al, PLoS Genet 2011). Now, with Illumina sequencing machines, his research group has developed secondary analysis software for variant detection; variant annotation (e.g., coding sequence changes resulting in synonymous or non-sysnonymous amino-acid changes, splice-site, etc); and has predicted effects of those changes. They have developed a specialized java user-interface, called VarSifter, for reviewing, sorting and filtering these annotated variants (Teer et al., Bioinformatics 2011). This secondary analysis pipeline is now integrated into NISC production operations for high-volume processing of whole-exome sequence data sets.
Other research in his group includes development of targeted capture methods (Teer et al., Genome Res 2010), RNA sequence analysis, and whole-genome sequence assembly (Pontius et al., Genome Res 2007; Mullikin et al., BMC Genomics 2010;Young et al. Genome Res 2010; Ryan et al., Science 2013). He has also collaborated with investigators outside of NIH on projects, such as the Neanderthal Genome Project with Svante Paabo, where his contribution to the analyses indicated that out-of-Africa modern human populations show ~3% admixture with Neanderthals (Green et al., Science 2010; Prüfer et al., Nature 2014). In collaboration with Stephan Schuster, he de novo assembled the genome of a Kalahari Bushman from 454 sequence data (Schuster et al., Nature 2010). Dr. Mullikin's research group is also involved at the advisory stage as projects come to NISC from numerous collaborators, and they actively participate in other large projects, like ClinSeq, the Undiagnosed Diseases Program, and the autism sequencing project.
Since becoming the acting director of NISC in December 2009, then director in September 2011, the interactions between his Comparative Genomics Analysis Unit and NISC complemented each other. As NISC's (acting) director, he effectively managed this large center during a particularly challenging time of rapid technology change, which has now seen next-generation sequencing throughput increase 20-fold. This growth has complemented Comparative Genomics Analysis Unit research directions, which continue to focus on the algorithmic reduction of large datasets into meaningful results.
Presently, Dr. Mullikin's research group is developing analysis methods for a number of collaborative projects. Together with Julie Segre, Ph.D., NHGRI, the group is developing whole-genome assembly methods for bacterial genomes. Unique genome peculiarities and a continually changing backdrop of sequencing technologies and methodologies present new assembly challenges with bacterial genomes.
In collaboration with Paul Liu, Ph.D., NHGRI, his group is looking at a whole-genome view of DNA sequence variations in human induced pluripotent stem cells generated with non-integrating plasmid vectors. Here they were able to detect somatic mutations locked into the stem cell lines at a rate of about one mutation per two-million bases, or around 1,300 mutations genome-wide.
With Yardena Samuels, Ph.D., formerly with NHGRI and currently at the Weizmann Institute of Science, Rehovot, Israel, and Daphne Bell, Ph.D., NHGRI, his group is developing statistically robust methods for detecting mutation patterns in tumors when compared to their matched normal samples. In collaboration with Patrick Duffy, M.D., at the National Insitute of Allergy and Infectious Diseases, his group assembled the genome of Plasmodium coatneyi from a single lane of HiSeq2000 data, which provided more than 500-fold coverage.
This assembly will enable future genomics research into this important non-human primate malaria species, which is an excellent model for the biology, immunology and pathology of humans infected with P. falciparum. In collaboration with Paul Wade at the National Institute of Environmental Health Science, his group is working on detecting whole-genome methylation patterns using Illumina sequencing of bisulfite treated DNA from mouse liver tissue.
This work will add this important new analytical capability for future research on methylation patterns in the study of organismal development, cellular development and cancer progression. RNA sequence analysis is another area of rapid analytical methods development, and they have been applying these methods to discover genes involved in coronary artery disease by examining the expression profiles and splice variant differences between RNA extracted from lymphoblastoid cell lines derived from ClinSeq subjects with high and low levels of coronary artery calcification.
The list of projects like these continues to grow as advances in genomic sequence technology coupled with an expanding array of analytical methods bring researchers to NISC and to his research group to find new ways to unlock the genomic mysteries currently hidden in their valuable samples. Dr. Mullikin looks forward to continuing these collaborative efforts and entering into many exciting new efforts as the genomics field rapidly evolves.
Voorhees WD, Bourland JD, Lamp ML, Mullikin JC, Geddes LA. Validation of the saline-dilution method for measuring cardiac output by simultaneous measurement with a perivascular electromagnetic flowprobe. Medical Instrumentation, 19(1):34-37. 1985. [PubMed]
Mullikin JC, Verbeek PW. Surface area estimation of digitized planes. Bioimaging, 1(1):6-16. 1993.
Mullikin JC, McMurray AA. Techview: DNA sequencing, Sequencing the Genome, Fast. Science, 283(5409):1867-9. 1999. [PubMed]
Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM, Burton J, Matthews LH, Pavitt R, Plumb RW, Sims SK, Ainscough RM, Attwood J, Bailey JM, Barlow K, Bruskiewich RM, Butcher PN, Carter NP, Chen Y, Clee CM, Coggill PC, Davies J, Davies RM, Dawson E, Francis MD, Joy AA, Lamble RG, Langford CF, Macarthy J, Mall V, Moreland A, Overton-Larty EK, Ross MT, Smith LC, Steward CA, Sulston JE, Tinsley EJ, Turney KJ, Willey DL, Wilson GD, McMurray AA, Dunham I, Rogers J, Bentley DR. An SNP Map of Human Chromosome 22. Nature, 407(6803):516-20. 2000. [PubMed]
The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature, 409(6822):860-921. 2001. [PubMed]
The International SNP Map Working Group. A map of human genome sequence variation containing 1.4 million single nucleotide polymorphisms. Nature, 409(6822):928-33. 2001. [PubMed]
Mullikin JC, Ning Z. The Phusion Assembler. Genome Res, 13(1):81-90. 2003. [PubMed]
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH. The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biol. 1(2): e45. 2003. [PubMed]
The International HapMap Consortium. The International HapMap Project. Nature. 426(6968):789-96. 2003. [PubMed]
The International HapMap Consortium. A haplotype map of the human genome. Nature, 437(7063):1299-320. 2005. [PubMed]
Ryan, J.F., Burton P.M., Mazza, M.E., Kwong, G.K., Mullikin, J.C., Finnerty, J.R. The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes. Evidence from the starlet sea anemone, Nematostella vectensis. Genome Biol, 7(7):R64. 2006. [PubMed]
Spencer CC, Deloukas P, Hunt S, Mullikin J, Myers S, Silverman B, Donnelly P, Bentley D, McVean G. The influence of recombination on human genetic diversity. PLoS Genet, 2(9):e148. 2006. [PubMed]
The Human Genome Structural Variation Working Group; Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, Lupski JR, Mullikin JC, Pritchard JK, Sebat J, Sherry ST, Smith D, Valle D, Waterston RH. Completing the map of human genetic variation. Nature. 447(7141):161-5. 2007. [PubMed]
Keinan A, Mullikin JC, Patterson N, Reich D. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet, 39(10):1251-5. 2007. [PubMed]
The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature, 449:851-861. 2007. [PubMed]
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES; International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archeveque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164):913-8. 2007. [PubMed]
Pontius JU, Mullikin JC, Smith DR; Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G; NISC Comparative Sequencing Program, O'Brien SJ. Initial sequence and comparative analysis of the cat genome. Genome Res, 17(11):1675-89. 2007. [PubMed]
Grice EA, Kong HH, Renaud G, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA. A diversity profile of the human skin microbiota. Genome Res, 18(7):1043-50. 2008. [PubMed]
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR and Eichler EE. Mapping and sequencing of structural variation from eight human genomes. Nature, 453:56-64. 2008. [PubMed]
Yuhki N, Mullikin JC, Beck T, Stephens R and O'Brien SJ. Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat. PLoS ONE, 3:e2674, 2008. [PubMed Central]
Keinan A, Mullikin JC, Patterson N and Reich D. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet, 41:66-70. 2009. [PubMed]
Sun JX, Mullikin JC, Patterson N, Reich DE. Microsatellites are molecular clocks that support accurate inferences about history. Mol Biol Evol, 26(5):1017-27. 2009. [PubMed]
Biesecker LG, Mullikin JC, Facio FM, Turner C, Cherukuri PF, Blakesley RW, Bouffard GG, Chines PS, Cruz P, Hansen NF, Teer JK, Maskeri B, Young AC; NISC Comparative Sequencing Program, Manolio TA, Wilson AF, Finkel T, Hwang P, Arai A, Remaley AT, Sachdev V, Shamburek R, Cannon RO, Green ED. The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine. Genome Res, 19(9):1665-74. 2009. [PubMed]
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res, 20(2):249-56. 2010. [PubMed]
Kang C, Riazuddin S, Mundorff J, Krasnewich D, Friedman P, Mullikin JC, Drayna D. Mutations in the Lysosomal Enzyme-Targeting Pathway and Persistent Stuttering. N Engl J Med, 362(8):677-85. 2010. [PubMed]
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Complete Khoisan and Bantu genomes from southern Africa. Nature, 18;463(7283):943-7. 2010. [PubMed]
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science, 328(5979):710-22. 2010. [PubMed]
Johnston JJ, Teer JK, Cherukuri PF, Hansen NF, Loftus SK; NIH Intramural Sequencing Center, Chong K, Mullikin JC, Biesecker LG. Massively Parallel Sequencing of Exons on the X Chromosome Identifies RBM10 as the Gene that Causes a Syndromic Form of Cleft Palate. Am J Hum Genet, 86(5):743-8. 2010. [PubMed]
Mullikin JC, Hansen NF, Shen L, Ebling H, Donahue WF, Tao W, Saranga DJ, Brand A, Rubenfield MJ, Young AC, Cruz P; NISC Comparative Sequencing Program, Driscoll C, David V, Al-Murrani SW, Locniskar MF, Abrahamsen MS, O'Brien SJ, Smith DR, Brockman JA. Light whole genome sequence for SNP discovery across domestic cat breeds. BMC Genomics, 11:406. 2010. [PubMed]
Teer JK, Mullikin JC. Exome Sequencing: The Sweet Spot Before Whole Genomes. Hum Mol Genet, Epub 2010 Aug 12. 2010. [PubMed]
Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ; NISC Comparative Sequencing Program, Margulies EH, Green ED, Collins FS, Mullikin JC, Biesecker LG. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res, 20(10):1420-31. 2010 [PubMed]
Ryan JF, Pang K; NISC Comparative Sequencing Program, Mullikin JC, Martindale MQ, Baxevanis AD. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. Evodevo, 1(1):9. 2010. [PubMed]
Davis EE, Zhang Q, Liu Q, Diplas BH, Davey LM, Hartley J, Stoetzel C, Szymanska K, Ramaswami G, Logan CV, Muzny DM, Young AC, Wheeler DA, Cruz P, Morgan M, Lewis LR, Cherukuri P, Maskeri B, Hansen NF, Mullikin JC, Blakesley RW, Bouffard GG; NISC Comparative Sequencing Program, Gyapay G, Rieger S, Tönshoff B, Kern I, Soliman NA, Neuhaus TJ, Swoboda KJ, Kayserili H, Gallagher TE, Lewis RA, Bergmann C, Otto EA, Saunier S, Scambler PJ, Beales PL, Gleeson JG, Maher ER, Attié-Bitach T, Dollfus H, Johnson CA, Green ED, Gibbs RA, Hildebrandt F, Pierce EA, Katsanis N. TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. Nat Genet. 43(3):189-96. 2011. [PubMed]
Wei X, Walia V, Lin JC, Teer JK, Prickett TD, Gartner J, Davis S, NISC Comparative Sequencing Program, Stemke-Hale K, Davies MA, Gershenwald JE, Robinson W, Robinson S, Rosenberg SA, Samuels Y. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet, 43(5)442-6. 2011. [PubMed]
Gunay-Aygun M, Falik-Zaccai TC, Vilboux T, Zivony-Elboum Y, Gumruk F, Cetin M, Khayat M, Boerkoel CF, Kfir N, Huang Y, Maynard D, Dorward H, Berger K, Kleta R, Anikster Y, Arat M, Freiberg AS, Kehrel BE, Jurk K, Cruz P, Mullikin JC, White JG, Huizing M, Gahl WA. NBEAL2 is mutated in gray platelet syndrome and is required for biogenesis of platelet ?-granules. Nat Genet, 43(8):732-4. 2011. [PubMed]
Solomon BD, Pineda-Alvarez DE, Hadley DW, NISC Comparative Sequencing Program, Teer JK, Cherukuri PF, Hansen NF, Cruz P, Young AC, Blakesley RW, Lanpher B, Mayfield Gibson S, Sincan M, Chandrasekharappa SC, Mullikin JC. Personalized genomic medicine: Lessons from the exome. Mol Genet Metab, 104(1-2):189-91. 2011. [PubMed]
Lindhurst MJ, Sapp JC, Teer JK, Johnston JJ, Finn EM, Peters K, Turner J, Cannons JL, Bick D, Blakemore L, Blumhorst C, Brockmann K, Calder P, Cherman N, Deardorff MA, Everman DB, Golas G, Greenstein RM, Kato BM, Keppler-Noreuil KM, Kuznetsov SA, Miyamoto RT, Newman K, Ng D, O'Brien K, Rothenberg S, Schwartzentruber DJ, Singhal V, Tirabosco R, Upton J, Wientroub S, Zackai EH, Hoag K, Whitewood-Neal T, Robey PG, Schwartzberg PL, Darling TN, Tosi LL, Mullikin JC, Biesecker LG. A Mosaic Activating Mutation in AKT1 Associated with the Proteus Syndrome. N Engl J Med. 365(7):611-9. 2011. [PubMed]
Wu X, Zhou T, Zhu J, Zhang B, Georgiev I, Wang C, Chen X, Longo NS, Louder M, McKee K, O'Dell S, Perfetto S, Schmidt SD, Shi W, Wu L, Yang Y, Yang ZY, Yang Z, Zhang Z, Bonsignori M, Crump JA, Kapiga SH, Sam NE, Haynes BF, Simek M, Burton DR, Koff WC, Doria-Rose N, Connors M; NISC Comparative Sequencing Program, Mullikin JC, Nabel GJ, Roederer M, Shapiro L, Kwong PD, Mascola JR. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing. Science, 333(6049):1593-602. [PubMed]
Bell DW, Sikdar N, Lee KY, Price JC, Chatterjee R, Park HD, Fox J, Ishiai M, Rudd ML, Pollock LM, Fogoros SK, Mohamed H, Hanigan CL; NISC Comparative Sequencing Program, Zhang S, Cruz P, Renaud G, Hansen NF, Cherukuri PF, Borate B, McManus KJ, Stoepel J, Sipahimalani P, Godwin AK, Sgroi DC, Merino MJ, Elliot G, Elkahloun A, Vinson C, Takata M, Mullikin JC, Wolfsberg TG, Hieter P, Lim DS, Myung K. Predisposition to cancer caused by genetic and functional defects of mammalian Atad5. PLoS Genet, 7(8):e1002245. 2011. [PubMed]
Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD, Lavrov DV. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. Mitochondrial DNA. 2011 Aug;22(4):130-42.
Biesecker LG, Shianna KV, Mullikin JC. Exome sequencing: the expert view. Genome Biol, 12(9):128. 2011. [PubMed]
Gahl WA, Markello TC, Toro C, Fajardo KF, Sincan M, Gill F, Carlson-Donohoe H, Gropman A, Pierson TM, Golas G, Wolfe L, Groden C, Godfrey R, Nehrebecky M, Wahl C, Landis DM, Yang S, Madeo A, Mullikin JC, Boerkoel CF, Tifft CJ, Adams D; for the NISC Comparative Sequencing Program. The National Institutes of Health Undiagnosed Diseases Program: Insights into rare diseases. Genet Med, 14(1):51-9. 2012. [PubMed]
Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM; NISC Comparative Sequencing Center, Mullikin JC, Gallagher PG, Hardison RC, Margulies EH, Bodine DM. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood, 118(17):e139-48. 2011. [PubMed]
Teer JK, Green ED, Mullikin JC, Biesecker LG. VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics, 28:599-600. 2011. [PubMed]
Rees MG, Ng D, Ruppert S, Turner C, Beer NL, Swift AJ, Morken MA, Below JE, Blech I, Mullikin JC, McCarthy MI, Biesecker LG, Gloyn AL, Collins FS. Correlation of rare coding variants in the gene encoding human glucokinase regulatory protein with phenotypic, cellular, and kinetic outcomes. J Clin Invest, 122(1):205-17. 2012. [PubMed]
Wang X, Mitra N, Cruz P, Deng L; NISC Comparative Sequencing Program, Varki N, Angata T, Green ED, Mullikin J, Hayakawa T, Varki A. Evolution of Siglec-11 and Siglec-16 Genes in Hominins. Mol Biol Evol, 29(8):2073-86. 2012. [PubMed]
Cheng L, Hansen NF, Zhao L, Du Y, Zou C, Donovan FX, Chou BK, Zhou G, Li S, Dowey SN, Ye Z; NISC Comparative Sequencing Program, Chandrasekharappa SC, Yang H, Mullikin JC, Liu PP. Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by nonintegrating plasmid expression. Cell Stem Cell, 10(3):337-44. 2012. [PubMed]
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388):169-75. [PubMed]
Solomon BD, Hadley DW, Pineda-Alvarez DE; NISC Comparative Sequencing Program, Kamat A, Teer JK, Cherukuri PF, Hansen NF, Cruz P, Young AC, Berkman BE, Chandrasekharappa SC, Mullikin JC. Incidental medical information in whole-exome sequencing. Pediatrics, 129(6):e1605-11. 2012. [PubMed]
Wang X, Mitra N, Secundino I, Banda K, Cruz P, Padler-Karavani V, Verhagen A, Reid C, Lari M, Rizzi E, Balsamo C, Corti G, De Bellis G, Longo L; NISC Comparative Sequencing Program, Beggs W, Caramelli D, Tishkoff SA, Hayakawa T, Green ED, Mullikin JC, Nizet V, Bui J, Varki A. Specific inactivation of two immunomodulatory SIGLEC genes during human evolution. Proc Natl Acad Sci U S A, 109(25):9935-40. 2012. [PubMed]
Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG. Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am J Hum Genet, 91(1):97-108.2012. [PubMed]
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404):527-31. 2012. [PubMed]
Coon SL, Munson PJ, Cherukuri PF, Sugden D, Rath MF, Møller M, Clokie SJ, Fu C, Olanich ME, Rangel Z, Werner T; NISC Comparative Sequencing Program, Mullikin JC, Klein DC. Circadian changes in long noncoding RNAs in the pineal gland. Proc Natl Acad Sci U S A, 109(33):13319-24. 2012. [PubMed]
Kaelin CB, Xu X, Hong LZ, David VA, McGowan KA, Schmidt-Küntzel A, Roelke ME, Pino J, Pontius J, Cooper GM, Manuel H, Swanson WF, Marker L, Harper CK, van Dyk A, Yue B, Mullikin JC, Warren WC, Eizirik E, Kos L, O'Brien SJ, Barsh GS, Menotti-Raymond M. Specifying and sustaining pigmentation patterns in domestic and wild cats. Science, 337(6101):1536-41. 2012. [PubMed]
Le Gallo M, O'Hara AJ, Rudd ML, Urick ME, Hansen NF, O'Neil NJ, Price JC, Zhang S, England BM, Godwin AK, Sgroi DC; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program, Hieter P, Mullikin JC, Merino MJ, Bell DW. Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nat Genet, 44(12):1310-5. 2012. [PubMed]
Prasad AB, Mullikin JC, Green ED; NISC Comparative Sequencing Program. A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence. Mol Phylogenet Evol. 2012 Dec 13
Alhaddad H, Khan R, Grahn RA, Gandolfi B, Mullikin JC, Cole SA, Gruffydd-Jones TJ, Häggström J, Lohi H, Longeri M, Lyons LA. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds. PLoS One, 8(1):e53537. 2013. [PubMed]
Giannuzzi G, Siswara P, Malig M, Marques-Bonet T; NISC Comparative Sequencing Program, Mullikin JC, Ventura M, Eichler EE. Evolutionary dynamism of the primate LRRC37 gene family. Genome Res, 23(1):46-59. 2013. [PubMed]
Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Becker J, Benjamin B, Blakesley R, Bouffard G, Brooks S, Coleman H, Dekhtyar M, Gregory M, Guan X, Gupta J, Han J, Hargrove A, Ho SL, Johnson T, Legaspi R, Lovett S, Maduro Q, Masiello C, Maskeri B, McDowell J, Montemayor C, Mullikin J, Park M, Riebow N, Schandler K, Schmidt B, Sison C, Stantripop M, Thomas J, Thomas P, Vemulapalli M, Young A, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013 Apr 3. 2013. [PubMed]
Teer JK, Johnston JJ, Anzick SL, Pineda M, Stone G, Meltzer PS, Mullikin JC, Biesecker LG. Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting. BMC Genomics, 14(1):253. 2013. [PubMed]
Kirino Y, Zhou Q, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, Ozyazgan Y, Ugurlu S, Erer B, Abaci N, Ustek D, Meguro A, Ueda A, Takeno M, Inoko H, Ombrello MJ, Satorius CL, Maskeri B, Mullikin JC, Sun HW, Gutierrez-Cruz G, Kim Y, Wilson AF, Kastner DL, Gül A, Remmers EF. Targeted resequencing implicates the familial Mediterranean fever gene MEFV and the toll-like receptor 4 gene TLR4 in Behcet disease. Proc Natl Acad Sci U S A, 110(20):8134-9. 2013. [PubMed]
Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC. Shimmer: detection of genetic alterations in tumors using next-generation sequence data. Bioinformatics, 29(12):1498-503. 2013. [PubMed]
Gandolfi B, Alhaddad H, Affolter VK, Brockman J, Haggstrom J, Joslin SE, Koehne AL, Mullikin JC, Outerbridge CA, Warren WC, Lyons LA. To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed. PLoS One, 8(6):e67105. 2013. [PubMed]
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. Great ape genetic diversity and population history. Nature. 2013 Jul 3. doi: 10.1038/nature12228. [PubMed]
Vilboux T, Lev A, Malicdan MC, Simon AJ, Järvinen P, Racek T, Puchalka J, Sood R, Carrington B, Bishop K, Mullikin J, Huizing M, Garty BZ, Eyal E, Wolach B, Gavrieli R, Toren A, Soudack M, Atawneh OM, Babushkin T, Schiby G, Cullinane A, Avivi C, Polak-Charcon S, Barshack I, Amariglio N, Rechavi G, van der Werff ten Bosch J, Anikster Y, Klein C, Gahl WA, Somech R. A congenital neutrophil defect syndrome associated with mutations in VPS45. N Engl J Med, 369(1):54-65. 2013. [PubMed]
Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK; NISC Comparative Sequencing Program, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y, Becker J, Benjamin B, Blakesley R, Bouffard G, Brooks S, Coleman H, Dekhtyar M, Gregory M, Guan X, Gupta J, Han J, Hargrove A, Ho SL, Johnson T, Legaspi R, Lovett S, Maduro Q, Masiello C, Maskeri B, McDowell J, Montemayor C, Mullikin J, Park M, Riebow N, Schandler K, Schmidt B, Sison C, Stantripop M, Thomas J, Thomas P, Vemulapalli M, Young A. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A, 110(33):13481-6. 2013. [PubMed]
Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N; NISC Comparative Sequencing Program, Black BL, Visel A, Pennacchio LA, Collins FS; National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Authors; NISC Comparative Sequencing Program Authors. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A, 110(44):17921-6. 2013. [PubMed]
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P; NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science, 342(6164):1242592. 2013. [PubMed]
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481):43-9. 2014. [PubMed]
Mullikin JC. The evolution of comparative genomics. Mol Genet Genomic Med, 2(5): 363-8. 2014. [PubMed]
Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med, 6(254): 254ra126. 2014. [PubMed]
LaFave MC, Varshney GK, Vemulapalli M, Mullikin JC, Burgess SM. A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1. Genetics, 98(1):167-70. 2014. [PubMed]
Callicrate T, Dikow R, Thomas JW, Mullikin JC, Jarvis ED, Fleischer RC, NISC Comparative Sequencing Program. Genomic resources for the endangered Hawaiian honeycreepers. BMC Genomics, 15:1098. 2014. [PubMed]
Huang HW, NISC Comparative Sequencing Program, Mullikin JC, Hansen NF. Evaluation of variant detection software for pooled next-generation sequence data. BMC Informatics, 16:235. 2015. [PubMed]
Hartley SW, Mullikin JC. QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. BMC Informatics, 16:225. 2015. [PubMed]
Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, Brooks BP, Brownell I, Candotti F, Gonsalves SG, Hart SP, Kong HH, Rother KI, Sokolic R, Solomon BD, Zein WM, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG. Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. Am J Hum Genet, 96(6):913-25. 2015. [PubMed]
Last updated: November 17, 2021